//
// Expansion Hunter
// Copyright 2016-2019 Illumina, Inc.
// All rights reserved.
//
// Author: Egor Dolzhenko <edolzhenko@illumina.com>,
// Concept: Michael Eberle <meberle@illumina.com>
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
//      http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
//

#include "genotyping/SmallVariantGenotype.hh"

using std::ostream;

namespace ehunter
{

ostream& operator<<(ostream& out, const SmallVariantGenotype& genotype)
{

    if (genotype.numAlleles() == 1)
    {
        out << (genotype.isHomRef() ? "0" : "1");
    }
    else
    {
        if (genotype.isHomRef())
        {
            out << "0/0";
        }
        else if (genotype.isHomAlt())
        {
            out << "1/1";
        }
        else
        {
            out << "0/1";
        }
    }

    return out;
}
}
